Houston proved it's on the rise as the Cougars notched its first 30+ win season since '08, finishing with a 36-22 record and tied Rice for the most non-conference wins at 22. The Cougars garnered C-USA Newcomer of the Year Frankie Ratcliff) and Freshman of the Year Justin Montemayor) honors, while having four named to C-USA Second Team (Montemayor, Ratcliff, Austin Pruitt, Kyle Survance) and four to the All-Freshman Team (Montemayor, Survance, Josh Vidales, Jake Lemoine). Montemayor and Survance went on to be named Louisville Slugger Freshman All-Americans. The team also notched a program-best 3.17 GPA in the fall, while 25 were named to C-USA Commissioner's Honor Roll. Montemayor and Caleb Barker were tabbed as C-USA Academic Medals and Barker and Daniel Poncedeleon earned Academic All-League honors. Houston senior ace Austin Pruitt tallied 10 wins for the first time since Brad Lincoln had 12 in 2006, while junior reliever Chase Wellbrock racked up 11 saves for the first time since Donnie Joseph had 11 in 2009. The Cougars jumped into the Top 25 national rankings for five weeks midseason - for the first time since 2006 and produced its best 25-game start since 1989 at 21-4.

Houston had a magical post season run, finishing ranked 30th in the nation in 2008 after capturing the C-USA Tournament title with five wins at the Championship. The Cougars went on to win three games at the College Station Regional, but would fall a win short to advance to a Super Regional. Bryan Pounds and Jake Stewart were First Team All-C-USA honorees, while Wes Musick was a Second Team selection. Chase Dempsay and Blake Kelso were honored as Freshman All-Americans by national publications and Bryan Pounds, Musick and Stewart were All-South Region honorees.

Houston had its second straight Super Regional appearance, winning the NCAA College Station Regional. The Cougars fell 1-2 in a three-game series at Reckling Park vs. Rice. Ryan Wagner earned six First Team All-American honors, while joiningBrad Sullivan on the All-South Region Team. Hyung Cho and Sullivan were First Team All-C-USA honorees, while Wagner earned Second Team honors. Matt Farrington and Travis Tully were recognized on the All-Freshman Team. Cole Bruce was named College Station MVP. Houston finished the year ranked No. 16 and saw seven players drafted, highlighted by two First Round draft picks in Wagner and Sullivan. Also drafted were Michael Bourn, Danny Zell, Brian Henderson, Brett Cooley, and Cho.

Houston had one of its most recent prolific runs in the post season, finishing ranked No. 9 in the final rankings. After winning the Conference USA Regular Season and Mesa Regional with a perfect 3-0 record, the Cougars fell 1-2 to Texas in the Austin Super Regional, as Texas went on to win the College World Series that season. Brad Sullivan was named Conference Pitcher of the Year and Chris Snyder was a Johnny Bench Catcher of the Year Finalist. Sullivan, Snyder and Jesse Crain were all First Team All-Americans, joined by Stuart Musslewhite as a Freshman All-American. Sullivan, Brett Cooley, Snyder and Crain were all First Team All-C-USA honorees, while Michael Bourn was a Second Team selection. Head Coach Rayner Noble was named South Central Region Coach of the Year and Keith Whatley was the Mesa Regional MVP. Wagner owned the NCAA single-season record with 16.8 strikeouts per nine innings. Crain and Snyder were Second Round selections in the draft, while Cooley, Whatley, and Nathan Mitchell were also drafted.

2000 marked the only year in C-USA where the Cougars notched the Regular Season and Tournament titles. The program hosted the Regional and Super Regional rounds at Cougar Field - claiming the Regional Championship with wins over Rice and Princeton. With the Regional Championship and Super Regional appearance against San Jose State, the Cougars finished No. 11 in the final national rankings. The team saw itself ranked in the Top 25 every week during the season and was ranked as high as No. 3 during the first week of March. The team won 18 of their last 22 games and swept series vs. No. 3 LSU and No. 5 USC during the regular season. RHP Kyle Crowell was named to five All-America Teams, while battery mate Jarrod Bitter was a NCBWA Second Team All-America selection. Freshman Bryan Harris was honored on Collegiate Baseball Freshman All-America Team. Head coach Rayner Noble was named C-USA Coach of the Year and Crowell was named C-USA Pitcher of the Year for the second straight season. The Cougars placed eight (3 - first, 5 - second) on the All-Conference squads and led the nation in fielding percentage (.977) and the league in homeruns (75), doubles (157), triples (16), runs scored (484), ERA (3.58) and slugging percentage (.484).

Houston claimed its first C-USA Regular Season title and went on to host its first NCAA Regional at Cougar Field during the 1999 season. The Cougars wrapped up the year ranked No. 24 nationally and jumped as high as No. 18 during the Regional appearance. Houston won 13 of its last 16 regular season games to finish 20-7 in C-USA play and capture the title. 1999 saw RHP Kyle Crowell, first baseman J.P.Woodward and outfielder Brandon Caraway receive All-America honors, while head coach Rayner Noble notched C-USA Coach of the Year and Crowell was awarded C-USA Pitcher of the Year honors. Houston had six named to the All-Conference Team. The Cougars notched wins over No. 1 Rice, No. 3 Texas A&M, No. 4 Texas and No. 10 Alabama during regular season play for its second 40+ win season since joining the league in 1997.

1997 marked the first season to play in Conference USA. The Cougars wrapped up a second place regular season finish with a 19-8 mark and went on to claim the C-USA Tournament title en route to an NCAA South I Regional in Baton Rouge, La. Houston was ranked No. 24 during postseason play and the Cougars saw outfielder Goefrey Tomlinson and third baseman Dustin Carr named to All-America Teams, while Shane Nance was named a Freshman All-American. Four were named to the C-USA All-Conference Team, while four were named to the All-Freshman Team.